RNA modification database
This RNA modification databases are a compilation of databases and web portals and servers used for RNA modification. RNA modification occurs in all living organisms, and is one of the most evolutionarily conserved properties of RNAs [1][2][3]. It can affect the activity, localization as well as stability of RNAs, and has been linked with human diseases [1][2][3].
RNA Modification Databases
| Name | Description | type | Link | References |
|---|---|---|---|---|
| RMBase | RMBase is designed for decoding the landscape of RNA modifications identified from high-throughput sequencing data (Pseudo-seq, Ψ-seq, CeU-seq, Aza-IP, MeRIP-seq, m6A-seq, miCLIP, m6A-CLIP, RiboMeth-seq). demonstrated thousands of RNA modifications located within mRNAs, regulatory ncRNAs (e.g. lncRNAs, miRNAs), miRNA target sites and disease-related SNPs. | database | website | [4] |
| MODOMICS | MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. | database | website | [5] |
| RNAMDB | RNAMDB has served as a focal point for information pertaining to naturally occurring RNA modifications | database | website | [6] |
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- ^ a b Li, S; Mason, CE (2013). "The pivotal regulatory landscape of RNA modifications". Annual review of genomics and human genetics. 15: 127–50. PMID 24898039.
- ^ a b Song, CX; Yi, C; He, C (October 2012). "Mapping recently identified nucleotide variants in the genome and transcriptome". Nature biotechnology. 30 (11): 1107–16. PMID 23138310.
- ^ a b Meyer, KD; Jaffrey, SR (April 2014). "The dynamic epitranscriptome: N6-methyladenosine and gene expression control". Nature reviews. Molecular cell biology. 15 (5): 313–26. PMID 24713629.
- ^ Sun, WJ; Li, JH; Liu, S; Wu, J; Zhou, H; Qu, LH; Yang, JH (11 October 2015). "RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data". Nucleic acids research. PMID 26464443.
- ^ Machnicka, MA; Milanowska, K; Osman Oglou, O; Purta, E; Kurkowska, M; Olchowik, A; Januszewski, W; Kalinowski, S; Dunin-Horkawicz, S; Rother, KM; Helm, M; Bujnicki, JM; Grosjean, H (December 2012). "MODOMICS: a database of RNA modification pathways--2013 update". Nucleic acids research. 41 (Database issue): D262-7. PMID 23118484.
- ^ Cantara, WA; Crain, PF; Rozenski, J; McCloskey, JA; Harris, KA; Zhang, X; Vendeix, FA; Fabris, D; Agris, PF (December 2010). "The RNA Modification Database, RNAMDB: 2011 update". Nucleic acids research. 39 (Database issue): D195-201. PMID 21071406.